Mini- and micro-satellites in the genome of rodent malaria parasites

Microsatellite markers and genetic mapping in Plasmodium falciparum

Whole-genome methods are changing the scope of biological questions that can be addressed in malaria research. In the rich context provided by Plasmodium falciparum genome sequencing, genetic mapping is a powerful tool for identifying genes involved in parasite development, invasion, transmission and drug resistance. The recent development of a high-resolution P. falciparum linkage map consisting of hundreds of microsatellite markers will facilitate an integrated genomic approach to understanding the relationship between genetic variations and biological phenotypes. Here, Michael Ferdig and Xin-zhuan Su provide an overview for applying microsatellite markers and genetic maps to gene mapping, parasite typing and studies of parasite population changes.

Short-sequence DNA repeats in prokaryotic genomes

Short-sequence DNA repeat (SSR) loci can be identified in all eukaryotic and many prokaryotic genomes. These loci harbor short or long stretches of repeated nucleotide sequence motifs. DNA sequence motifs in a single locus can be identical and/or heterogeneous. SSRs are encountered in many different branches of the prokaryote kingdom. They are found in genes encoding products as diverse as microbial surface components recognizing adhesive matrix molecules and specific bacterial virulence factors such as lipopolysaccharide-modifying enzymes or adhesins. SSRs enable genetic and consequently phenotypic flexibility. SSRs function at various levels of gene expression regulation. Variations in the number of repeat units per locus or changes in the nature of the individual repeat sequences may result from recombination processes or polymerase inadequacy such as slipped-strand mispairing (SSM), either alone or in combination with DNA repair deficiencies. These rather complex phenomena can occur with relative ease, with SSM approaching a frequency of 10(-4) per bacterial cell division and allowing high-frequency genetic switching. Bacteria use this random strategy to adapt their genetic repertoire in response to selective environmental pressure. SSR-mediated variation has important implications for bacterial pathogenesis and evolutionary fitness. Molecular analysis of changes in SSRs allows epidemiological studies on the spread of pathogenic bacteria. The occurrence, evolution and function of SSRs, and the molecular methods used to analyze them are discussed in the context of responsiveness to environmental factors, bacterial pathogenicity, epidemiology, and the availability of full-genome sequences for increasing numbers of microorganisms, especially those that are medically relevant.

Finding genetic markers for complex phenotypic traits in parasites

The identification, mapping and eventual cloning of genes which determine or influence important epidemiological traits in parasites can have great benefits for the control of parasitic disease. In this review, strategies are outlined for identifying genetic markers for complex, quantitative traits. A genetic marker is a variable DNA sequence which co-occurs with a variable quantitative trait. Candidate markers are chosen because they are thought to directly influence the trait whereas random markers are expected to be linked to another DNA sequence which influences the trait. Association studies compare the value of a quantitative trait between different marker genotype classes in a population, without regard to family structure. Linkage studies compare the value of a quantitative trait between marker genotype classes within families or within a population (usually derived from a cross between inbred lines) which is segregating for both marker and quantitative trait loci. The most commonly used analytical methods for determining the significance of association or linkage between marker and quantitative trait loci, and for estimating parameters such as recombination rate and quantitative gene action, are least-squares and maximum likelihood. Both methods may be used to test either single markers or the interval between flanking markers, and both suffer from the need to minimize type I and type II error rates with multiple tests.

Minisatellites corresponding to the human polycore probes 33.6 and 33.15 in the genome of the most 'primitive' known eukaryote Giardia lamblia

DNA fingerprinting has been widely used for genetic characterization and individual recognition in a range of species, from man and other mammals down the evolutionary scale to some lower eukaryotic parasites. These techniques utilise repetitive elements first characterised in the human genome, known as minisatellites, which display extensive allelic variability. Few biological or biochemical characteristics have been found that distinguish isolates of Giardia lamblia (Gl), or their apparent variations in virulence. We have characterized 21 Gl isolates in axenic culture using DNA fingerprinting with the human minisatellite probes, 33.6 and 33.15. Up to 12 variable bands per isolate were recognized in the size range of 2.5 to 15 kb by Southern blot hybridization of restriction endonuclease-digested Gl DNA. Most isolates demonstrated a distinct banding pattern or DNA fingerprint. The results suggest that this method may provide a basis for the detailed genotypic characterization of Gl which will be amenable to computer and statistical analysis for use in studies of virulence and epidemiology. Also, as Gl occupies a unique phylogenetic position as a member of the earliest known divergence from the eukaryotic line of descent, this study may provide a useful model for the study of other important eukaryotic pathogens, as it is rapidly becoming apparent that minisatellites are ubiquitous components of eukaryotic genomes.

Structural organisation of microsatellite families in the Leishmania genome and polymorphisms at two (CA)n loci

In the present study, we have analysed the frequency and distribution of several microsatellite DNAs [(CA)n, (GGT)n and (GCA)n] in the genome of Leishmania. Hybridisation analysis on the molecular karyotypes of different Leishmania strains showed the presence of these three microsatellites on all chromosomes of the parasite. The number of microsatellite clusters appeared grossly similar among strains from different Old World complexes. However, these three microsatellite families showed an uneven distribution among heterologous chromosomes of the same strain. Moreover, restriction analysis of chromosome I in various strains of Leishmania infantum showed a strong clustering of these microsatellites in the same chromosomal region. A partial genomic library was screened with a (CA)n probe, and 21 positive clones were isolated. The sequencing of these clones confirmed the association of various microsatellites such as (CA)n, (CT)n, and (GCA)n. Finally, specific polymerase chain reaction amplification of two cloned (CA)n loci demonstrated allelic size polymorphisms among strains within L. infantum and Leishmania donovani. Most of the 34 strains analysed were found to be monoallelic, while two alleles were found in a small number of strains. The interest of these sequences for studies on ploidy and population genetics of the parasite is discussed.

DNA fingerprinting of medically important microorganisms by use of PCR

Selected segments of any DNA molecule can be amplified exponentially by PCR. This technique provides a powerful tool to detect and identify minimal numbers of microorganisms. PCR is applicable both in diagnosis and in epidemiology. By amplification of hypervariable DNA domains, differences can be detected even among closely related strains. PCR fingerprinting is a valuable tool for medical microbiologists, epidemiologists, and microbial taxonomists. The current state of PCR-mediated genotyping is reviewed, and a comparison with conventional molecular typing methods is included. Because of its speed and versatility, PCR fingerprinting will play an important role in microbial genetics, epidemiology, and systematics.

Genotyping isolates and clones of Giardia duodenalis by polymerase chain reaction: implications for the detection of genetic variation among protozoan parasite species

Detection of genetic variation among microorganisms can be done by DNA fingerprinting using the polymerase chain reaction (PCR). Application of primers directed to polymorphic DNA leads to the amplification of DNA fragments which differ in length when different species or isolates of a single species are compared. It has been demonstrated that PCR primers resembling eukaryotic repeat motifs enable the straightforward genetic differentiation of Giardia duodenalis isolates. Depending on the repeat motif, genetic variation between cloned G. duodenalis lines could also be detected. DNA polymorphisms could also be detected by random amplification of polymorphic DNA (RAPD) analyses. When the results obtained for G. duodenalis are compared to those found for another protozoan parasite, Naegleria fowleri, clear differences are encountered. In contrast to the findings for G. duodenalis, the repeat motif primers did not allow the discrimination of 'N. fowleri isolates. Apparently, as determined by this PCR-mediated genotyping, genetic variation occurs in G. duodenalis with increased frequency at the isolate level as compared to N. fowleri. The possible implications of this observation for clonality or the definition of a species in protozoan parasites will be discussed.

Development of DNA probes for the ovine Eimeria species E. crandallis and E. ovinoidalis

As an alternative to morphological speciation, DNA probes have been developed to identify Eimeria crandallis and E. ovinoidalis, the species associated with ovine coccidiosis. Coccidia-free lambs were infected with pure cultures of E. crandallis and E. ovinoidalis. Oocysts separated from faeces were sporulated and treated to release sporozoites from which DNA was purified. Repetitive DNA sequences were identified by hybridisation and cloned. The specificity of selected clones was tested by hybridisation with dot blots of four other ovine Eimeria species, a mixture of caprine Eimeria species and E. acervulina of the chicken. The probes allowed the detection of DNA equivalent to that present in approximately 1,500 oocysts. To increase the sensitivity of the test, a polymerase chain reaction (PCR) approach was adopted, using oligonucleotide primers specific for the cloned repeats. By this method, less than 10 oocysts of E. ovinoidalis could be reliably detected. In addition to the species-specific probes, other highly repetitive DNA sequences from E. crandallis and E. ovinoidalis were cloned and sequenced; these repeats hybridised to all ovine, caprine and avian Eimeria species tested and contained tandem CGA and putative telomeric repeats.